From 5811ab93d856bb339a35eef2d23266fcb781cbe7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 17 Feb 2023 21:50:07 +0100 Subject: Update benchmark results for 7950X --- .travis.yml | 1 + log/build.log | 2 +- vignettes/FOCUS_D.html | 6 +- vignettes/FOCUS_L.html | 50 ++++++------ vignettes/mkin.html | 2 +- vignettes/web_only/benchmarks.R | 1 + vignettes/web_only/benchmarks.html | 134 +++++++++++++++++--------------- vignettes/web_only/benchmarks.rmd | 3 +- vignettes/web_only/mkin_benchmarks.rda | Bin 1656 -> 1810 bytes vignettes/web_only/saem_benchmarks.html | 132 +++++++++++++++++++++++-------- vignettes/web_only/saem_benchmarks.rda | Bin 477 -> 710 bytes vignettes/web_only/saem_benchmarks.rmd | 3 +- 12 files changed, 210 insertions(+), 124 deletions(-) diff --git a/.travis.yml b/.travis.yml index 64c27426..a30182aa 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,6 +8,7 @@ jobs: os: linux env: + DRAT_REPOS: "jranke" global: - USE_BSPM="true" - NOT_CRAN="true" diff --git a/log/build.log b/log/build.log index db5fac76..e077c30c 100644 --- a/log/build.log +++ b/log/build.log @@ -6,5 +6,5 @@ * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ‘mkin/vignettes/web_only’ -* building ‘mkin_1.3.0.tar.gz’ +* building ‘mkin_1.2.3.tar.gz’ diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index d1d51ddb..43c4f1fa 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -449,10 +449,10 @@ the mkinparplot function.

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
-
## mkin version used for fitting:    1.3.0 
+
## mkin version used for fitting:    1.2.2 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Fri Feb 17 10:41:52 2023 
-## Date of summary: Fri Feb 17 10:41:52 2023 
+## Date of fit:     Fri Feb 17 20:04:31 2023 
+## Date of summary: Fri Feb 17 20:04:31 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 190ab65b..ed150c0a 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -1561,10 +1561,10 @@ model fit. This covers the numerical analysis given in the FOCUS
 report.

 
m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)

-
## mkin version used for fitting:    1.3.0 
+
## mkin version used for fitting:    1.2.2 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Fri Feb 17 10:41:53 2023 
-## Date of summary: Fri Feb 17 10:41:53 2023 
+## Date of fit:     Fri Feb 17 20:04:32 2023 
+## Date of summary: Fri Feb 17 20:04:32 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -1664,17 +1664,17 @@ checked.

 
## Warning in sqrt(1/diag(V)): NaNs produced

 
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful

-
## mkin version used for fitting:    1.3.0 
+
## mkin version used for fitting:    1.2.2 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Fri Feb 17 10:41:53 2023 
-## Date of summary: Fri Feb 17 10:41:53 2023 
+## Date of fit:     Fri Feb 17 20:04:32 2023 
+## Date of summary: Fri Feb 17 20:04:32 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 369 model solutions performed in 0.026 s
+## Fitted using 369 model solutions performed in 0.025 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1810,17 +1810,17 @@ plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")

 

 
summary(m.L2.FOMC, data = FALSE)

-
## mkin version used for fitting:    1.3.0 
+
## mkin version used for fitting:    1.2.2 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Fri Feb 17 10:41:54 2023 
-## Date of summary: Fri Feb 17 10:41:54 2023 
+## Date of fit:     Fri Feb 17 20:04:32 2023 
+## Date of summary: Fri Feb 17 20:04:32 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.015 s
+## Fitted using 239 model solutions performed in 0.014 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1891,10 +1891,10 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")

 

 
summary(m.L2.DFOP, data = FALSE)

-
## mkin version used for fitting:    1.3.0 
+
## mkin version used for fitting:    1.2.2 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Fri Feb 17 10:41:54 2023 
-## Date of summary: Fri Feb 17 10:41:54 2023 
+## Date of fit:     Fri Feb 17 20:04:32 2023 
+## Date of summary: Fri Feb 17 20:04:32 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1903,7 +1903,7 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.04 s
+## Fitted using 581 model solutions performed in 0.039 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2004,10 +2004,10 @@ as a row index and datasets as a column index.

 using square brackets for indexing which will result in the use of the
 summary and plot functions working on mkinfit objects.

 
summary(mm.L3[["DFOP", 1]])

-
## mkin version used for fitting:    1.3.0 
+
## mkin version used for fitting:    1.2.2 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Fri Feb 17 10:41:54 2023 
-## Date of summary: Fri Feb 17 10:41:54 2023 
+## Date of fit:     Fri Feb 17 20:04:33 2023 
+## Date of summary: Fri Feb 17 20:04:33 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2126,17 +2126,17 @@ well. The error level at which the χ2
 
summary(mm.L4[["SFO", 1]], data = FALSE)

-
## mkin version used for fitting:    1.3.0 
+
## mkin version used for fitting:    1.2.2 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Fri Feb 17 10:41:54 2023 
-## Date of summary: Fri Feb 17 10:41:54 2023 
+## Date of fit:     Fri Feb 17 20:04:33 2023 
+## Date of summary: Fri Feb 17 20:04:33 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.009 s
+## Fitted using 142 model solutions performed in 0.008 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2190,10 +2190,10 @@ negligible.

 ##        DT50 DT90
 ## parent  106  352

 
summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version used for fitting:    1.3.0 
+
## mkin version used for fitting:    1.2.2 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Fri Feb 17 10:41:54 2023 
-## Date of summary: Fri Feb 17 10:41:54 2023 
+## Date of fit:     Fri Feb 17 20:04:33 2023 
+## Date of summary: Fri Feb 17 20:04:33 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/vignettes/mkin.html b/vignettes/mkin.html
index ec3bf5da..a16f3074 100644
--- a/vignettes/mkin.html
+++ b/vignettes/mkin.html
@@ -1614,7 +1614,7 @@ div.tocify {
 
 
Introduction to mkin

 
Johannes Ranke

-
Last change 15 February 2021 (rebuilt 2023-02-13)

+
Last change 15 February 2021 (rebuilt 2023-02-17)

 
 
 
diff --git a/vignettes/web_only/benchmarks.R b/vignettes/web_only/benchmarks.R
index 6c9b133e..46081ca9 100644
--- a/vignettes/web_only/benchmarks.R
+++ b/vignettes/web_only/benchmarks.R
@@ -20,6 +20,7 @@ cpu_model <- benchmarkme::get_cpu()$model_name
 cpu_model <- gsub("AMD ", "", cpu_model)
 cpu_model <- gsub("Intel\\(R\\) Core\\(TM\\) ", "", cpu_model)
 cpu_model <- gsub(" Eight-Core Processor", "", cpu_model)
+cpu_model <- gsub(" 16-Core Processor", "", cpu_model)
 cpu_model <- gsub(" CPU @ 2.50GHz", "", cpu_model)
 
 operating_system <- Sys.info()[["sysname"]]
diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html
index 6cce41e6..0800ac48 100644
--- a/vignettes/web_only/benchmarks.html
+++ b/vignettes/web_only/benchmarks.html
@@ -1592,7 +1592,7 @@ div.tocify {
 
 
Benchmark timings for mkin

 
Johannes Ranke

-
Last change 14 July 2022 (rebuilt 2023-02-17)

+
Last change 17 February 2023 (rebuilt 2023-02-17)

 
 
 
@@ -1679,14 +1679,6 @@ systems. All trademarks belong to their respective owners.

 
Constant variance (t1) and two-component error model (t2) for four
 models fitted to two datasets, i.e. eight fits for each test.

 
--------
@@ -1852,19 +1844,27 @@ models fitted to two datasets, i.e. eight fits for each test.

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 OS
 

 

 LinuxRyzen 9 7950X 16-Core ProcessorRyzen 9 7950X
 4.2.21.2.21.3081.7931.2.01.2881.794
 

 

 LinuxRyzen 9 7950X 16-Core ProcessorRyzen 9 7950X
 4.2.21.3.01.2871.8051.2.21.2761.804
LinuxRyzen 9 7950X4.2.21.2.31.3271.863
 

 
 

@@ -1875,15 +1875,6 @@ models fitted to two datasets, i.e. eight fits for each test.

 by variable (t5) for three models fitted to one dataset, i.e. three fits
 for each test.

 
---------
@@ -2069,21 +2060,30 @@ for each test.

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 OS
 

 

 LinuxRyzen 9 7950X 16-Core ProcessorRyzen 9 7950X
 4.2.21.2.20.7832.3641.2301.2.00.7922.3781.245
 

 

 LinuxRyzen 9 7950X 16-Core ProcessorRyzen 9 7950X
 4.2.21.3.00.7311.9841.1001.2.20.7842.3551.233
LinuxRyzen 9 7950X4.2.21.2.30.7582.0501.135
 

 
 

@@ -2095,16 +2095,16 @@ and variance by variable (t10 and t11) for one model fitted to one
 dataset, i.e. one fit for each test.

 ---+++++++++------
@@ -2351,27 +2351,39 @@ dataset, i.e. one fit for each test.

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 LinuxRyzen 9 7950X 16-Core ProcessorRyzen 9 7950X
 4.2.21.2.20.4420.5820.6581.1710.8011.0931.2.00.4450.5910.6601.1900.8141.100
 

 

 LinuxRyzen 9 7950X 16-Core ProcessorRyzen 9 7950X
 4.2.21.3.00.4000.5180.5800.9900.7010.9351.2.20.4430.5860.6611.1760.8031.097
LinuxRyzen 9 7950X4.2.21.2.30.4140.5330.5981.0200.7260.966
 

 
 

diff --git a/vignettes/web_only/benchmarks.rmd b/vignettes/web_only/benchmarks.rmd
index 117dc96a..132e5062 100644
--- a/vignettes/web_only/benchmarks.rmd
+++ b/vignettes/web_only/benchmarks.rmd
@@ -1,7 +1,7 @@
 ---
 title: "Benchmark timings for mkin"
 author: "Johannes Ranke"
-date: Last change 14 July 2022 (rebuilt `r Sys.Date()`)
+date: Last change 17 February 2023 (rebuilt `r Sys.Date()`)
 output:
   html_document:
     toc: true
@@ -47,6 +47,7 @@ cpu_model <- benchmarkme::get_cpu()$model_name
 cpu_model <- gsub("AMD ", "", cpu_model)
 cpu_model <- gsub("Intel\\(R\\) Core\\(TM\\) ", "", cpu_model)
 cpu_model <- gsub(" Eight-Core Processor", "", cpu_model)
+cpu_model <- gsub(" 16-Core Processor", "", cpu_model)
 cpu_model <- gsub(" CPU @ 2.50GHz", "", cpu_model)
 
 operating_system <- Sys.info()[["sysname"]]
diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
index a9a4adbf..0a88d04f 100644
Binary files a/vignettes/web_only/mkin_benchmarks.rda and b/vignettes/web_only/mkin_benchmarks.rda differ
diff --git a/vignettes/web_only/saem_benchmarks.html b/vignettes/web_only/saem_benchmarks.html
index a3bbafef..83e70e79 100644
--- a/vignettes/web_only/saem_benchmarks.html
+++ b/vignettes/web_only/saem_benchmarks.html
@@ -1592,7 +1592,7 @@ div.tocify {
 
 
Benchmark timings for saem.mmkin

 
Johannes Ranke

-
Last change 14 November 2022 (rebuilt 2023-02-17)

+
Last change 17 February 2023 (rebuilt 2023-02-17)

 
 
 
@@ -1815,24 +1815,44 @@ systems. All trademarks belong to their respective owners.

 4.851
 
 
-Ryzen 9 7950X 16-Core Processor
+Ryzen 9 7950X
+Linux
+1.2.1
+3.2
+1.352
+2.813
+2.401
+2.074
+
+
+Ryzen 9 7950X
 Linux
 1.2.2
 3.2
-1.470
-2.263
-1.840
-2.299
+1.328
+2.738
+2.336
+2.023
+
+
+Ryzen 9 7950X
+Linux
+1.2.3
+3.2
+1.711
+2.028
+2.868
+2.361
 
 
 Ryzen 9 7950X 16-Core Processor
 Linux
-1.3.0
+1.2.3
 3.2
-1.181
-2.199
-2.057
-1.909
+1.444
+2.485
+2.738
+2.946
 
 
 
@@ -1882,24 +1902,44 @@ systems. All trademarks belong to their respective owners.

 8.401
 
 
-Ryzen 9 7950X 16-Core Processor
+Ryzen 9 7950X
+Linux
+1.2.1
+3.2
+2.388
+3.033
+3.532
+3.310
+
+
+Ryzen 9 7950X
 Linux
 1.2.2
 3.2
-2.118
-3.528
-3.295
-3.157
+2.341
+2.968
+3.465
+3.341
+
+
+Ryzen 9 7950X
+Linux
+1.2.3
+3.2
+2.347
+3.175
+3.426
+3.588
 
 
 Ryzen 9 7950X 16-Core Processor
 Linux
-1.3.0
+1.2.3
 3.2
-2.384
-3.124
-3.484
-3.518
+2.228
+3.332
+3.257
+3.306
 
 
 
@@ -1944,20 +1984,36 @@ systems. All trademarks belong to their respective owners.

 798.580
 
 
-Ryzen 9 7950X 16-Core Processor
+Ryzen 9 7950X
+Linux
+1.2.1
+3.2
+11.247
+285.216
+
+
+Ryzen 9 7950X
 Linux
 1.2.2
 3.2
-12.336
-277.666
+11.242
+284.258
+
+
+Ryzen 9 7950X
+Linux
+1.2.3
+3.2
+11.724
+216.900
 
 
 Ryzen 9 7950X 16-Core Processor
 Linux
-1.3.0
+1.2.3
 3.2
-12.082
-214.433
+11.604
+215.890
 
 
 
@@ -1991,18 +2047,32 @@ systems. All trademarks belong to their respective owners.

 1312.445
 
 
-Ryzen 9 7950X 16-Core Processor
+Ryzen 9 7950X
+Linux
+1.2.1
+3.2
+489.939
+
+
+Ryzen 9 7950X
 Linux
 1.2.2
 3.2
-459.051
+482.970
+
+
+Ryzen 9 7950X
+Linux
+1.2.3
+3.2
+389.119
 
 
 Ryzen 9 7950X 16-Core Processor
 Linux
-1.3.0
+1.2.3
 3.2
-392.885
+401.477
 
 
 
diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda
index 7d060f91..564c851b 100644
Binary files a/vignettes/web_only/saem_benchmarks.rda and b/vignettes/web_only/saem_benchmarks.rda differ
diff --git a/vignettes/web_only/saem_benchmarks.rmd b/vignettes/web_only/saem_benchmarks.rmd
index 6e51fa66..6aeefd7f 100644
--- a/vignettes/web_only/saem_benchmarks.rmd
+++ b/vignettes/web_only/saem_benchmarks.rmd
@@ -1,7 +1,7 @@
 ---
 title: "Benchmark timings for saem.mmkin"
 author: "Johannes Ranke"
-date: Last change 14 November 2022 (rebuilt `r Sys.Date()`)
+date: Last change 17 February 2023 (rebuilt `r Sys.Date()`)
 output:
   html_document:
     toc: true
@@ -31,6 +31,7 @@ cpu_model <- benchmarkme::get_cpu()$model_name
 cpu_model <- gsub("AMD ", "", cpu_model)
 cpu_model <- gsub("Intel\\(R\\) Core\\(TM\\) ", "", cpu_model)
 cpu_model <- gsub(" Eight-Core Processor", "", cpu_model)
+cpu_model <- gsub(" 16-Core Processor", "", cpu_model)
 cpu_model <- gsub(" CPU @ 2.50GHz", "", cpu_model)
 
 operating_system <- Sys.info()[["sysname"]]
-- 
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